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Yorodumi- PDB-1w7g: Alpha-thrombin complex with sulfated hirudin (residues 54-65) and... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1w7g | ||||||
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Title | Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- Arginine template inhibitor CS107 | ||||||
Components |
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Keywords | HYDROLASE/HYDROLASE INHIBITOR / BLOOD COAGULATION-INHIBITOR / THROMBIN / ARGATROBAN / SERINE PROTEASE / COAGULATION / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin ...positive regulation of lipid kinase activity / cytolysis by host of symbiont cells / positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway / thrombospondin receptor activity / Defective factor XII causes hereditary angioedema / thrombin / regulation of blood coagulation / neutrophil-mediated killing of gram-negative bacterium / ligand-gated ion channel signaling pathway / Defective F8 cleavage by thrombin / Platelet Aggregation (Plug Formation) / negative regulation of astrocyte differentiation / negative regulation of platelet activation / positive regulation of collagen biosynthetic process / negative regulation of cytokine production involved in inflammatory response / positive regulation of blood coagulation / negative regulation of fibrinolysis / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / regulation of cytosolic calcium ion concentration / fibrinolysis / Intrinsic Pathway of Fibrin Clot Formation / Peptide ligand-binding receptors / positive regulation of release of sequestered calcium ion into cytosol / acute-phase response / Regulation of Complement cascade / negative regulation of proteolysis / Cell surface interactions at the vascular wall / positive regulation of receptor signaling pathway via JAK-STAT / lipopolysaccharide binding / growth factor activity / serine-type endopeptidase inhibitor activity / positive regulation of insulin secretion / platelet activation / response to wounding / positive regulation of protein localization to nucleus / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / positive regulation of reactive oxygen species metabolic process / blood coagulation / antimicrobial humoral immune response mediated by antimicrobial peptide / Thrombin signalling through proteinase activated receptors (PARs) / heparin binding / regulation of cell shape / positive regulation of cell growth / G alpha (q) signalling events / collagen-containing extracellular matrix / blood microparticle / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell surface receptor signaling pathway / positive regulation of protein phosphorylation / G protein-coupled receptor signaling pathway / endoplasmic reticulum lumen / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of cell population proliferation / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) HIRUDO MEDICINALIS (medicinal leech) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å | ||||||
Authors | Remiche, J. / Sauvage, E. / Herman, R. / Charlier, P. | ||||||
Citation | Journal: Org.Biomol.Chem. / Year: 2005 Title: Design, Synthesis and Evaluation of Graftable Thrombin Inhibitors for the Preparation of Blood-Compatible Polymer Materials. Authors: Salvagnini, C. / Michaux, C. / Remiche, J. / Wouters, J. / Charlier, P. / Marchand-Brynaert, J. #1: Journal: J.Biol.Chem. / Year: 1991 Title: Crystallographic Analysis at 3.0-A Resolution of the Binding to Human Thrombin of Four Active Site-Directed Inhibitors Authors: Banner, D.W. / Hadvary, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1w7g.cif.gz | 82.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1w7g.ent.gz | 61 KB | Display | PDB format |
PDBx/mmJSON format | 1w7g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1w7g_validation.pdf.gz | 835.9 KB | Display | wwPDB validaton report |
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Full document | 1w7g_full_validation.pdf.gz | 848.4 KB | Display | |
Data in XML | 1w7g_validation.xml.gz | 17 KB | Display | |
Data in CIF | 1w7g_validation.cif.gz | 23.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w7/1w7g ftp://data.pdbj.org/pub/pdb/validation_reports/w7/1w7g | HTTPS FTP |
-Related structure data
Related structure data | 1hgtS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29780.219 Da / Num. of mol.: 1 / Fragment: THROMBIN HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: PLASMA / References: UniProt: P00734, thrombin |
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#2: Protein/peptide | Mass: 1526.553 Da / Num. of mol.: 1 / Fragment: SULFATED, RESIDUES 60 TO 71 / Source method: obtained synthetically / Source: (synth.) HIRUDO MEDICINALIS (medicinal leech) / References: UniProt: P09945 |
#3: Protein/peptide | Mass: 4096.534 Da / Num. of mol.: 1 / Fragment: THROMBIN LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Cell: PLASMA / References: UniProt: P00734, thrombin |
#4: Chemical | ChemComp-MIU / |
#5: Water | ChemComp-HOH / |
Sequence details | CHAIN I HAS CONFLICT AT POSITION 54 WHERE THE UNIPROT ENTRY (P09945) HAS GLY IN THE SEQUENCE. |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.58 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: VAPOUR DIFFUSION HANGING DROP 20% P5KMME 0.1M HEPES PH7.5 0.3M NACL THROMBIN 10MG/ML HIRUDIN 3MM AND CS107 16MM, PH 7.50 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9797 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Apr 14, 2003 / Details: MIRRORS |
Radiation | Monochromator: SI111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9797 Å / Relative weight: 1 |
Reflection | Resolution: 1.65→24.85 Å / Num. obs: 40937 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Biso Wilson estimate: 16.2 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 4.8 |
Reflection shell | Resolution: 1.65→1.69 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.6 / % possible all: 93 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1HGT Resolution: 1.65→19.78 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1249943.7 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 39.38 Å2 / ksol: 0.41 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.65→19.78 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.65→1.75 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
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Xplor file |
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